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revision 1827, Wed Apr 25 22:22:41 2007 UTC revision 2137, Mon Mar 17 22:21:24 2008 UTC
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1    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
4            functionality; barely tested in
5            * tests/factorizing.R
6    
7            * src/Csparse.c (diag_tC): new functionality to enable faster
8            determinant(<dsCMatrix>, .) in
9            * R/dsCMatrix.R
10    
11    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
12    
13            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
14              src/CHMfactor.c, src/CHMfactor.h,
15              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
16              Log-determinant of the parent matrix from a CHMfactor object as
17              chm_factor_ldetL2; documentation and support
18    
19    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
22    
23    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
26            warning.
27    
28    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
31    
32            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
33              <diagonal> o <sparse_triangular>
34              setAs(., "nMatrix") added.
35    
36            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
37    
38            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
39                    new argument 'checkDense = FALSE'.
40    
41    
42    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
45            back-permutation of the matrix exponential.
46    
47            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
48    
49            * DESCRIPTION (Date,Version): ready to release 0.999375-5
50    
51            * tests/simple.R: testing diagN2U
52    
53    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/Auxiliaries.R (diagN2U): interface to
56    
57            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
58    
59            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
60    
61    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * src/chm_common.c (chm_diagN2U): new utility.
64    
65            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
66            make use of chm_diagN2U() and hence now preserve triangularity and
67            unit-triangularity.
68    
69            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
70    
71    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
74    
75            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
76            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
77    
78            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
79    
80            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
81    
82            * src/chm_common.c (AS_CHM_FINISH): add note about problem
83            for triangular (diag = "U").
84    
85    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
88            * R/bind.R:  .Call(dense_to_Csparse, *)
89    
90    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/Matrix.R (Matrix): no longer use coercions to specific classes
93                    (since we are discouraging them in user code).
94    
95            * tests/*.R: also replaces coercions to specific classes by
96            coercions to super classes.
97    
98            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
99    
100    
101    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
104    
105            * src/dense.c (dense_band): generalized from ddense_band
106    
107            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
108              now for "denseMatrix" (instead of just "ddense*"); much
109              simplified setMethod()s for these.
110    
111            * src/dense.c (dense_to_symmetric): generalized from ddense_*
112    
113    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
116            version of as(*, "symmetricMatric").
117    
118            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
119            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
120    
121    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/Matrix.R (subset.ij): utility, as first step to faster
124               M [ <ij-matrix> ] indexing.
125    
126            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
127    
128            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
129            for more efficient symmpart() and skewpart() methods.
130    
131            * src/Mutils.c (equal_string_vectors): utility
132    
133            * src/dense.c (ddense_to_symmetric): new function used in
134    
135            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
136    
137            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
138            order to match the generic (and evade .local(..)).
139    
140            * R/dsCMatrix.R: dgC -> dsC: use C code!
141    
142            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
143            as per TODO
144    
145            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
146    
147            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
148    
149    
150    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
153    
154            * R/Auxiliaries.R (non0.i): take out of non0ind
155    
156            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
157            make tril(), triu(), band() work for "matrix" and all "dense*"
158    
159            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
160            * tests/simple.R: test the fix above
161    
162            * R/sparseMatrix.R ([): simplification: no coerce to <general>
163                    before we use as(., <Tsparse>)[...] anyway
164    
165            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
166    
167            * R/triangularMatrix.R (isTriangular): methods for all subclasses
168            instead of "triangularMatrix" -- just to disambiguate
169    
170    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
173            * tests/indexing.R: example that fails above
174    
175    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
178            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
179                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
180    
181            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
182            * src/Tsparse.h, init.c: ditto
183            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
184                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
185            * R/sparseMatrix.R (isTriangular): hence simplified
186    
187    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Ops.R (.Arith.Csparse): new utility factored out of former
190              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
191    
192    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
195    
196            * inst/test-tools.R (isOrthogonal): new function; also file restructured
197    
198    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
201            coercion to "nMatrix" and "pMatrix"
202    
203            * R/AllClass.R: "Schur" class;  "number" class union
204            * man/number-class.Rd:
205            * man/Schur-class.Rd:
206    
207            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
208            (.simpleSchur): Schur() method for diagonal matrices
209            (.triSchur):    Schur() method for triangular matrices
210            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
211    
212    
213    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
216    
217    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
220                    in order to ensure 'system = *' is not lost;
221                    formals()$system instead of cut&paste.
222            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
223    
224    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * DESCRIPTION (Date): make ready for release --> 0.999375-4
227    
228            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
229    
230    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
233                    and hence does as.vector(.).
234            * man/pMatrix-class.Rd: docs
235            * R/sparseMatrix.R: fix for printing "integer sparse"
236    
237            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
238    
239            * R/Matrix.R and others: use "exact" function argument list for
240                    both "["   : (x, i,j, ..., drop)
241                    and  "[<-" : (x, i,j, ..., value)
242    
243            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
244            * R/Tsparse.R (replTmat):    ditto
245            * R/diagMatrix.R (replDiag): ditto
246            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
247            * tests/indexing.R: testing the above
248    
249    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/sparseMatrix.R (cov2cor): method for sparse matrices
252    
253            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
254    
255            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
256    
257            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
258    
259    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/Matrix.R: "generic" cov2cor() method
262    
263            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
264                    speed up Q %*% D %*% t(Q)
265            * tests/dpoMatrix.R: test nearPD()
266    
267    2007-12-05  Doug Bates and Martin Maechler
268    
269            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
270            stats::xtabs() allowing to create sparse matrices.
271    
272    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
275    
276    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
279    
280    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/LU.R: solve() method for "denseLU"
283    
284    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * DESCRIPTION (Version): 0.999375-3 preparing for release
287    
288            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
289    
290            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
291    
292    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
295              thanks to Kasper Kristensen.
296            * tests/matprod.R: regression test for that.
297    
298    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
299    
300            * [r4778] R/AllGeneric.R: Check R version before defining generics for
301              primitives
302    
303    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/denseMatrix.R (rcond): method
306            * R/sparseQR.R (rcond): method, use x or t(x)
307    
308    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
311            matrices.
312            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
313    
314            * man/rcond.Rd: mention the more general definition, and add
315            example for non-square matrices.
316    
317            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
318    
319    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
322    
323    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
326            * tests/indexing.R: add new regression for the above cases.
327    
328    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * src/Mutils.h (__sun): clause for alloca.h on Solaris
331    
332    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * DESCRIPTION (Date, Version): 0.999375-2
335    
336    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/HBMM.R (readMM): make work for pattern matrices as well
339    
340    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
341    
342            * [r4730] src/Mutils.h: declare alloca
343            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
344              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
345              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
346              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
347              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
348              methods; switch writeMM to use CHOLMOD code; repair readMM
349    
350    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
353            Oehlschlaegel's ... result type still to be discussed!
354    
355    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * man/image-methods.Rd: new, combining all image() methods
358    
359    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
362            to work via dgC...
363    
364            * R/Matrix.R (Matrix): special treatment for "table" (S3)
365    
366    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/dgTMatrix.R (image): change defaults to
369                    aspect = "iso", colorkey = FALSE
370    
371    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
374            must copy its *expanded* x slot before LAPACK call.
375    
376            * tests/matprod.R: test the last days' changes.
377    
378    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
379    
380            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
381              as well as in sources
382            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
383              Lapack call
384    
385    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
388                    ("Matrix", "matrix") which is needed in some cases.
389            Ditto for solve().
390    
391            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
392            infinite recursion in dispatch for some cases.
393    
394    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
395    
396            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
397              so pointers match
398    
399    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * DESCRIPTION (Date): set ready for release -- 0.999375-1
402    
403    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
404    
405            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
406              src/chm_common.c, src/chm_common.h: Change API for
407              numeric_as_chm_dense and N_AS_CHM_DN
408    
409    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
412            * tests/matprod.R: regr.test for it
413    
414    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
417            * tests/group-methods.R: and regression-test it
418    
419    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
420    
421            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
422              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
423              triplet_to_sparse, documentation, use typedefs
424    
425    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * man/dpoMatrix-class.Rd: added 'corMatrix' example
428    
429            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
430            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
431            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
432    
433            * R/lsparseMatrix.R: bug fix in "all" method
434            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
435    
436            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
437            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
438                    + matrix |-> nMatrix coercion
439            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
440            * man/pMatrix-class.Rd: ditto
441    
442            * R/Matrix.R (Summary): method for non-dMatrix
443    
444            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
445            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
446                    test all Summary methods.
447    
448    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
451    
452    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
455    
456            * R/pMatrix.R (t?crossprod): methods for pMatrix
457    
458    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
459    
460            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
461    
462    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
463    
464            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
465              trying to fix a subtle bug - which has been somewhere else.
466    
467    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
468    
469            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
470              solve the bug
471    
472    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * src/dgCMatrix.c (compressed_to_TMatrix):
475    
476    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * src/Csparse.c (Rsparse_validate): new, to have some validity
479            checking for RsparseMatrix
480            * src/dgCMatrix.c (xRMatrix_validate): ditto
481            * src/dtCMatrix.c (tRMatrix_validate): ditto
482    
483    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
484    
485            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
486              lgRMatrix
487            * [r4568] DESCRIPTION: Prepare for bug-fix release
488            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
489              for declaration of cholmod_symmetry
490    
491    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
494            release.
495    
496    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
497    
498            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
499              functions - no longer used
500            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
501              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
502              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
503              Alloca
504    
505    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
506    
507            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
508              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
509              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
510              src/t_gCMatrix_colSums.c: more R_CheckStack()s
511    
512    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
513    
514            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
515              the required amount of memory then call M_numeric_as_chm_dense.
516            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
517              (like Calloc but calling alloca)
518    
519    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
522            and extended with more sophisticated 'col.names' option.
523            * NAMESPACE: export  printSparseMatrix()
524            * man/printSpMatrix.Rd: document, incl. examples
525    
526    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
527    
528            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
529              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
530              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
531    
532    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * DESCRIPTION (Version): 0.99875-4
535    
536            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
537            some dimnames perservation.
538    
539            * R/dsTMatrix.R (t-method): keep dimnames
540            * R/dtTMatrix.R:  ditto
541    
542            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
543            and ncol(.) < 10
544    
545            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
546            from Mutils.h
547    
548            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
549            e.g. in as(<ngCMatrix>, "matrix")
550    
551    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
552    
553            * [r4529] .: Create a branch for the API changes from the 0.99875
554              series to the 0.999375 series
555            * [r4530] DESCRIPTION, inst/include/Matrix.h,
556              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
557              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
558              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
559              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
560              as_cholmod_x functions
561    
562    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
563    
564            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
565              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
566              to Comparisons
567    
568    >>>>>>> .merge-right.r4561
569    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * DESCRIPTION (Version): 0.99875-3 ready to be released.
572    
573            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
574    
575            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
576            that should also work in a future version of R.
577    
578    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
579    
580            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
581    
582            * R/sparseVector.R: more *sparseVector coercions, notably for
583            non - double ones.
584    
585    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
588              notably the new ones building on the new .Call(.)s:
589    
590            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
591            all 4 of [dlin]gCMatrix_colSums().
592    
593    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
594    
595            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
596            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
597              result
598    
599    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * R/kronecker.R: fix typo (could lead to inf.recursion)
602            * test/simple.R: testing that
603    
604            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
605            method as well (which can have arguments, show() can't).
606    
607    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
608    
609            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
610              added dgCMatrix_colSums for [col,row][Sums,Means]
611    
612    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
613    
614            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
615              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
616              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
617            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
618              class
619            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
620              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
621              row names to store the levels - duh!  Added an example.
622    
623    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * src/Csparse.c (Csparse_validate): check for *repeated* entries
626            thanks to example from Christian Buchta; with a test here:
627            * tests/simple.R:
628    
629    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
632            of colSums(*, sparseResult = TRUE)
633    
634    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
637            'na.rm = FALSE' as "everywhere" else in R.
638    
639    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
640    
641            * [r4421] src/CSparse_install.sh: Modify for new organization of
642              CSparse package
643            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
644              SuiteSparse
645            * [r4426] src/Makefile: add ./UFconfig to the include path for
646              compilation
647            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
648            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
649              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
650    
651    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
654            * R/sparseMatrix.R (prSpMatrix): now gives a message about
655            suppressed column names.
656    
657    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
658    
659            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
660              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
661              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
662              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
663              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
664              Remove warnings after change to const char* CHAR
665    
666    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
667    
668            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
669              type of M_cholmod_ssmult
670    
671    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
672    
673            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
674              src/init.c: Yet another cholmod export - cholmod_ssmult
675    
676    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * NAMESPACE: exported drop0(), since
679            * man/drop0.Rd: I have seen several cases, I really wanted to use
680            it, so our users may want too.
681    
682    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * man/colSums.Rd: separately document colSums() etc, since these
685            have the extra argument 'sparseResult'.
686    
687    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
690            * man/spMatrix.Rd: docu., including examples
691    
692            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
693            in order to make colMeans() etc fast *and* correct.
694            * R/sparseVector.R (replSPvec): "[<-" functionality for
695            sparseVectors; tested in
696            * tests/simple.R:
697    
698    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
701            (very) sparse Matrices; output similar to Matlab's print().
702    
703    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
704    
705            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
706            0-based, indices (Jose Quesada <quesada@gmail.com>).
707    
708    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
709    
710            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
711    
712    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
713    
714            * R/Auxiliaries.R (sparsapply): new utility, much faster than
715            tapply1() for large sparse matrices.
716    
717    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
718    
719            * R/Matrix.R (dim<-): reshape now via sparseVector.
720    
721            * R/sparseVector.R: methods and function for
722            * R/AllClass.R: new "sparseVector" class and daughters.
723            * NAMESPACE: export new classes
724    
725    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * DESCRIPTION (Version): 0.99875-1
728            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
729    
730    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
733            indexing
734            * tests/indexing.R: test set for that.
735    
736    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
738            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
739            entries.
740            * tests/indexing.R(out): add regression test for it
741    
742    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
745            name for "!" method definitions.
746    
747    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * R/Tsparse.R (intI): new utility, used for "[" :
750                    Cleanup up there, and fixes for duplicated indices - more TODO!
751    
752            * tests/indexing.R(out): more tests
753    
754  2007-04-25  Douglas Bates  <bates@stat.wisc.edu>  2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
755    
756          * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack          * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
# Line 6  Line 759 
759          * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export          * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
760          cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).          cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
761    
762    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
765    
766    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
767    
768            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
769            up with extraneous names '0'...'<n-1>'
770    
771  2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773          * R/dgTMatrix.R (mat2dgT): care about NAs          * R/dgTMatrix.R (mat2dgT): care about NAs

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